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Searched refs:qfin1 (Results 1 – 25 of 46) sorted by relevance

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/dports/biology/bbmap/bbmap/current/jgi/
H A DPartitionReads.java112 qfin1=parser.qfin1; in PartitionReads()
133 if(qfin1!=null && qfin2==null && qfin1.indexOf('#')>-1 && !new File(qfin1).exists()){ in PartitionReads()
134 qfin2=qfin1.replace("#", "2"); in PartitionReads()
135 qfin1=qfin1.replace("#", "1"); in PartitionReads()
242 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
373 private String qfin1=null; field in PartitionReads
H A DBBQC.java98 qfin1=b; in BBQC()
378 …final String in1s=stripDirs(in1), in2s=stripDirs(in2), qfin1s=stripDirs(qfin1), qfin2s=stripDirs(q… in process()
381 ktrim(in1, in2, out1s, out2s, qfin1, qfin2, qfout1s, qfout2s, trimPrefix); in process()
495 if(qfin1!=null){argList.add("qfin1="+qfin1);} in ktrim()
556 …private void filter(String in1, String in2, String out1, String out2, String qfin1, String qfin2, … in filter() argument
588 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in filter()
655 …private void dehumanize(String in1, String in2, String out1, String out2, String qfin1, String qfi… in dehumanize() argument
701 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in dehumanize()
737 …private void normalize(String in1, String in2, String out1, String out2, String qfin1, String qfin… in normalize() argument
788 …if(qfin1!=null){argList.add("qfin1="+(prependIndir ? (tmpDir==null ? outDir : tmpDir) : "")+inPref… in normalize()
[all …]
H A DAdjustHomopolymers.java89 qfin1=parser.qfin1; in AdjustHomopolymers()
183 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
283 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
459 private String qfin1=null; field in AdjustHomopolymers
H A DKeepBestCopy.java108 qfin1=parser.qfin1; in KeepBestCopy()
139 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in makeCris()
258 private String qfin1=null; field in KeepBestCopy
H A DFungalRelease.java143 qfin1 = parser.qfin1; in FungalRelease()
200 cris = ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process()
433 private String qfin1 = null; field in FungalRelease
H A DKmerCountMulti.java137 qfin1=parser.qfin1; in KmerCountMulti()
216 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
466 private String qfin1=null;
H A DMakeChimeras.java96 qfin1=parser.qfin1; in MakeChimeras()
130 cris=ConcurrentReadInputStream.getReadInputStream(readsIn, false, ffin1, null, qfin1, null); in process()
335 private String qfin1=null; field in MakeChimeras
H A DReplaceHeaders.java113 qfin1=parser.qfin1; in ReplaceHeaders()
219 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
401 private String qfin1=null; field in ReplaceHeaders
H A DKExpand.java87 qfin1=parser.qfin1; in KExpand()
246 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
373 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
787 private String qfin1=null; field in KExpand
H A DTranslateSixFrames.java123 qfin1=parser.qfin1; in TranslateSixFrames()
197 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process()
368 private String qfin1=null; field in TranslateSixFrames
H A DCorrelateBarcodes.java108 qfin1=parser.qfin1; in CorrelateBarcodes()
180 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
382 private String qfin1=null; field in CorrelateBarcodes
H A DCountBarcodes.java128 qfin1=parser.qfin1; in CountBarcodes()
202 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
375 private String qfin1=null; field in CountBarcodes
H A DMergeBarcodes.java111 qfin1=parser.qfin1; in MergeBarcodes()
286 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in mergeWithMap()
404 private String qfin1=null; field in MergeBarcodes
/dports/biology/bbmap/bbmap/current/aligner/
H A DAllToAll.java81 qfin1=parser.qfin1; in AllToAll()
144 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
200 …reads=ConcurrentReadInputStream.getReads(maxReads, true, ffin1, null, qfin1, null); //TODO: Note … in process()
393 private String qfin1=null;
/dports/biology/bbmap/bbmap/current/template/
H A DA_Sample.java85 qfin1=parser.qfin1; in A_Sample()
175 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
275 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in makeCris()
402 private String qfin1=null; field in A_Sample
H A DA_SampleMT.java85 qfin1=parser.qfin1; in A_SampleMT()
178 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
288 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
494 private String qfin1=null;
H A DA_Sample_Unpaired.java102 qfin1=parser.qfin1; in A_Sample_Unpaired()
135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process()
222 private String qfin1=null; field in A_Sample_Unpaired
H A DBBTool_ST.java103 qfin1=parser.qfin1; in BBTool_ST()
268 if(!Tools.testForDuplicateFiles(true, in1, in2, qfin1, qfin2, out1, out2, qfout1, qfout2)){ in startup()
276 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in startup()
409 protected String qfin1=null; field in BBTool_ST
/dports/biology/bbmap/bbmap/current/prok/
H A DSplitRibo.java84 qfin1=parser.qfin1; in SplitRibo()
174 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
300 …Stream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null);
562 private String qfin1=null;
H A DRiboMaker.java91 qfin1=parser.qfin1; in RiboMaker()
186 qfin1=Tools.fixExtension(qfin1); in fixExtensions()
372 …ream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2);
626 private String qfin1=null;
/dports/biology/bbmap/bbmap/current/tax/
H A DFilterByTaxa.java115 qfin1=parser.qfin1; in FilterByTaxa()
214 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
368 private String qfin1=null; field in FilterByTaxa
/dports/biology/bbmap/bbmap/current/driver/
H A DLoadReads.java113 qfin1=parser.qfin1; in LoadReads()
177 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
388 private String qfin1=null; field in LoadReads
/dports/biology/bbmap/bbmap/current/hiseq/
H A DPlotFlowCell.java133 qfin1=parser.qfin1; in PlotFlowCell()
234 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in loadKmers()
259 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in fillTiles()
516 private String qfin1=null; field in PlotFlowCell
/dports/biology/bbmap/bbmap/current/sort/
H A DShuffle.java139 qfin1=parser.qfin1; in Shuffle()
213 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process()
384 private String qfin1=null; field in Shuffle
/dports/biology/bbmap/bbmap/current/sketch/
H A DKmerLimit.java150 qfin1=parser.qfin1; in KmerLimit()
255 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process()
579 private String qfin1=null; field in KmerLimit

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